ID code: '2M8K' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 9 C1' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' U A 3 alpha beta 73 93 79 76 108 C1' U A 4 alpha beta 103 123 109 106 138 C1' U A 5 alpha beta 133 153 139 136 168 C1' C A 6 alpha beta 163 183 169 166 200 C1' U A 7 alpha beta 195 215 201 198 230 C1' U A 8 alpha beta 225 245 231 228 260 C1' U A 9 alpha beta 255 275 261 258 290 C1' U A 10 alpha beta 285 305 291 288 320 C1' U A 11 alpha beta 315 335 321 318 350 C1' A A 12 alpha beta 345 367 351 348 383 C1' G A 13 alpha beta 378 401 384 381 417 C1' U A 14 alpha beta 412 432 418 415 447 C1' G A 15 alpha beta 442 465 448 445 481 C1' A A 16 alpha beta 476 498 482 479 514 C1' U A 17 alpha beta 509 529 515 512 544 C1' U A 18 alpha beta 539 559 545 542 574 C1' U A 19 alpha beta 569 589 575 572 604 C1' U A 20 alpha beta 599 619 605 602 634 C1' U A 21 alpha beta 629 649 635 632 664 C1' C A 22 alpha beta 659 679 665 662 695 C1' C A 23 alpha beta 690 710 696 693 726 C1' A A 24 alpha beta 721 743 727 724 759 C1' A A 25 alpha beta 754 776 760 757 792 C1' A A 26 alpha beta 787 809 793 790 825 C1' C A 27 alpha beta 820 840 826 823 856 C1' C A 28 alpha beta 851 871 857 854 887 C1' C A 29 alpha beta 882 902 888 885 918 C1' C A 30 alpha beta 913 933 919 916 949 C1' U A 31 alpha beta 944 964 950 947 979 C1' U A 32 alpha beta 974 994 980 977 1009 C1' U A 33 alpha beta 1004 1024 1010 1007 1039 C1' G A 34 alpha beta 1034 1057 1040 1037 1073 C1' U A 35 alpha beta 1068 1088 1074 1071 1103 C1' G A 36 alpha beta 1098 1121 1104 1101 1137 C1' C A 37 alpha beta 1132 1152 1138 1135 1168 C1' A A 38 alpha beta 1163 1185 1169 1166 1201 C1' A A 39 alpha beta 1196 1218 1202 1199 1234 C1' A A 40 alpha beta 1229 1251 1235 1232 1267 C1' A A 41 alpha beta 1262 1284 1268 1265 1300 C1' A A 42 alpha beta 1295 1317 1301 1298 1333 C1' U A 43 alpha beta 1328 1348 1334 1331 1363 C1' C A 44 alpha beta 1358 1378 1364 1361 1394 C1' A A 45 alpha beta 1389 1411 1395 1392 1427 C1' U A 46 alpha beta 1422 1442 1428 1425 1457 C1' U A 47 alpha beta 1452 1472 1458 1455 1487 C1' A A 48 alpha beta 1482 1505 1488 1485 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' U A 3 OK OK 78 74 91 77 106 C2' U A 4 OK OK 108 104 121 107 136 C2' U A 5 OK OK 138 134 151 137 166 C2' C A 6 OK OK 168 164 181 167 198 C2' U A 7 OK OK 200 196 213 199 228 C2' U A 8 OK OK 230 226 243 229 258 C2' U A 9 OK OK 260 256 273 259 288 C2' U A 10 OK OK 290 286 303 289 318 C2' U A 11 OK OK 320 316 333 319 348 C2' A A 12 OK OK 350 346 365 349 381 C2' G A 13 OK OK 383 379 399 382 415 C2' U A 14 OK OK 417 413 430 416 445 C2' G A 15 OK OK 447 443 463 446 479 C2' A A 16 OK OK 481 477 496 480 512 C2' U A 17 OK OK 514 510 527 513 542 C2' U A 18 OK OK 544 540 557 543 572 C2' U A 19 OK OK 574 570 587 573 602 C2' U A 20 OK OK 604 600 617 603 632 C2' U A 21 OK OK 634 630 647 633 662 C2' C A 22 OK OK 664 660 677 663 693 C2' C A 23 OK OK 695 691 708 694 724 C2' A A 24 OK OK 726 722 741 725 757 C2' A A 25 OK OK 759 755 774 758 790 C2' A A 26 OK OK 792 788 807 791 823 C2' C A 27 OK OK 825 821 838 824 854 C2' C A 28 OK OK 856 852 869 855 885 C2' C A 29 OK OK 887 883 900 886 916 C2' C A 30 OK OK 918 914 931 917 947 C2' U A 31 OK OK 949 945 962 948 977 C2' U A 32 OK OK 979 975 992 978 1007 C2' U A 33 OK OK 1009 1005 1022 1008 1037 C2' G A 34 OK OK 1039 1035 1055 1038 1071 C2' U A 35 OK OK 1073 1069 1086 1072 1101 C2' G A 36 OK OK 1103 1099 1119 1102 1135 C2' C A 37 OK OK 1137 1133 1150 1136 1166 C2' A A 38 OK OK 1168 1164 1183 1167 1199 C2' A A 39 OK OK 1201 1197 1216 1200 1232 C2' A A 40 OK OK 1234 1230 1249 1233 1265 C2' A A 41 OK OK 1267 1263 1282 1266 1298 C2' A A 42 OK OK 1300 1296 1315 1299 1331 C2' U A 43 OK OK 1333 1329 1346 1332 1361 C2' C A 44 OK OK 1363 1359 1376 1362 1392 C2' A A 45 OK OK 1394 1390 1409 1393 1425 C2' U A 46 OK OK 1427 1423 1440 1426 1455 C2' U A 47 OK OK 1457 1453 1470 1456 1485 C2' A A 48 OK OK 1487 1483 1503 1486 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' U A 3 OK OK 72 90 75 76 104 C3' U A 4 OK OK 102 120 105 106 134 C3' U A 5 OK OK 132 150 135 136 164 C3' C A 6 OK OK 162 180 165 166 196 C3' U A 7 OK OK 194 212 197 198 226 C3' U A 8 OK OK 224 242 227 228 256 C3' U A 9 OK OK 254 272 257 258 286 C3' U A 10 OK OK 284 302 287 288 316 C3' U A 11 OK OK 314 332 317 318 346 C3' A A 12 OK OK 344 364 347 348 379 C3' G A 13 OK OK 377 398 380 381 413 C3' U A 14 OK OK 411 429 414 415 443 C3' G A 15 OK OK 441 462 444 445 477 C3' A A 16 OK OK 475 495 478 479 510 C3' U A 17 OK OK 508 526 511 512 540 C3' U A 18 OK OK 538 556 541 542 570 C3' U A 19 OK OK 568 586 571 572 600 C3' U A 20 OK OK 598 616 601 602 630 C3' U A 21 OK OK 628 646 631 632 660 C3' C A 22 OK OK 658 676 661 662 691 C3' C A 23 OK OK 689 707 692 693 722 C3' A A 24 OK OK 720 740 723 724 755 C3' A A 25 OK OK 753 773 756 757 788 C3' A A 26 OK OK 786 806 789 790 821 C3' C A 27 OK OK 819 837 822 823 852 C3' C A 28 OK OK 850 868 853 854 883 C3' C A 29 OK OK 881 899 884 885 914 C3' C A 30 OK OK 912 930 915 916 945 C3' U A 31 OK OK 943 961 946 947 975 C3' U A 32 OK OK 973 991 976 977 1005 C3' U A 33 OK OK 1003 1021 1006 1007 1035 C3' G A 34 OK OK 1033 1054 1036 1037 1069 C3' U A 35 OK OK 1067 1085 1070 1071 1099 C3' G A 36 OK OK 1097 1118 1100 1101 1133 C3' C A 37 OK OK 1131 1149 1134 1135 1164 C3' A A 38 OK OK 1162 1182 1165 1166 1197 C3' A A 39 OK OK 1195 1215 1198 1199 1230 C3' A A 40 OK OK 1228 1248 1231 1232 1263 C3' A A 41 OK OK 1261 1281 1264 1265 1296 C3' A A 42 OK OK 1294 1314 1297 1298 1329 C3' U A 43 OK OK 1327 1345 1330 1331 1359 C3' C A 44 OK OK 1357 1375 1360 1361 1390 C3' A A 45 OK OK 1388 1408 1391 1392 1423 C3' U A 46 OK OK 1421 1439 1424 1425 1453 C3' U A 47 OK OK 1451 1469 1454 1455 1483 C3' A A 48 OK OK 1481 1501 1484 1485 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' U A 3 OK OK 74 89 71 73 102 C4' U A 4 OK OK 104 119 101 103 132 C4' U A 5 OK OK 134 149 131 133 162 C4' C A 6 OK OK 164 179 161 163 194 C4' U A 7 OK OK 196 211 193 195 224 C4' U A 8 OK OK 226 241 223 225 254 C4' U A 9 OK OK 256 271 253 255 284 C4' U A 10 OK OK 286 301 283 285 314 C4' U A 11 OK OK 316 331 313 315 344 C4' A A 12 OK OK 346 363 343 345 377 C4' G A 13 OK OK 379 397 376 378 411 C4' U A 14 OK OK 413 428 410 412 441 C4' G A 15 OK OK 443 461 440 442 475 C4' A A 16 OK OK 477 494 474 476 508 C4' U A 17 OK OK 510 525 507 509 538 C4' U A 18 OK OK 540 555 537 539 568 C4' U A 19 OK OK 570 585 567 569 598 C4' U A 20 OK OK 600 615 597 599 628 C4' U A 21 OK OK 630 645 627 629 658 C4' C A 22 OK OK 660 675 657 659 689 C4' C A 23 OK OK 691 706 688 690 720 C4' A A 24 OK OK 722 739 719 721 753 C4' A A 25 OK OK 755 772 752 754 786 C4' A A 26 OK OK 788 805 785 787 819 C4' C A 27 OK OK 821 836 818 820 850 C4' C A 28 OK OK 852 867 849 851 881 C4' C A 29 OK OK 883 898 880 882 912 C4' C A 30 OK OK 914 929 911 913 943 C4' U A 31 OK OK 945 960 942 944 973 C4' U A 32 OK OK 975 990 972 974 1003 C4' U A 33 OK OK 1005 1020 1002 1004 1033 C4' G A 34 OK OK 1035 1053 1032 1034 1067 C4' U A 35 OK OK 1069 1084 1066 1068 1097 C4' G A 36 OK OK 1099 1117 1096 1098 1131 C4' C A 37 OK OK 1133 1148 1130 1132 1162 C4' A A 38 OK OK 1164 1181 1161 1163 1195 C4' A A 39 OK OK 1197 1214 1194 1196 1228 C4' A A 40 OK OK 1230 1247 1227 1229 1261 C4' A A 41 OK OK 1263 1280 1260 1262 1294 C4' A A 42 OK OK 1296 1313 1293 1295 1327 C4' U A 43 OK OK 1329 1344 1326 1328 1357 C4' C A 44 OK OK 1359 1374 1356 1358 1388 C4' A A 45 OK OK 1390 1407 1387 1389 1421 C4' U A 46 OK OK 1423 1438 1420 1422 1451 C4' U A 47 OK OK 1453 1468 1450 1452 1481 C4' A A 48 OK OK 1483 1500 1480 1482 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' U A 3 OK OK 70 87 88 72 101 C5' U A 4 OK OK 100 117 118 102 131 C5' U A 5 OK OK 130 147 148 132 161 C5' C A 6 OK OK 160 177 178 162 193 C5' U A 7 OK OK 192 209 210 194 223 C5' U A 8 OK OK 222 239 240 224 253 C5' U A 9 OK OK 252 269 270 254 283 C5' U A 10 OK OK 282 299 300 284 313 C5' U A 11 OK OK 312 329 330 314 343 C5' A A 12 OK OK 342 361 362 344 376 C5' G A 13 OK OK 375 395 396 377 410 C5' U A 14 OK OK 409 426 427 411 440 C5' G A 15 OK OK 439 459 460 441 474 C5' A A 16 OK OK 473 492 493 475 507 C5' U A 17 OK OK 506 523 524 508 537 C5' U A 18 OK OK 536 553 554 538 567 C5' U A 19 OK OK 566 583 584 568 597 C5' U A 20 OK OK 596 613 614 598 627 C5' U A 21 OK OK 626 643 644 628 657 C5' C A 22 OK OK 656 673 674 658 688 C5' C A 23 OK OK 687 704 705 689 719 C5' A A 24 OK OK 718 737 738 720 752 C5' A A 25 OK OK 751 770 771 753 785 C5' A A 26 OK OK 784 803 804 786 818 C5' C A 27 OK OK 817 834 835 819 849 C5' C A 28 OK OK 848 865 866 850 880 C5' C A 29 OK OK 879 896 897 881 911 C5' C A 30 OK OK 910 927 928 912 942 C5' U A 31 OK OK 941 958 959 943 972 C5' U A 32 OK OK 971 988 989 973 1002 C5' U A 33 OK OK 1001 1018 1019 1003 1032 C5' G A 34 OK OK 1031 1051 1052 1033 1066 C5' U A 35 OK OK 1065 1082 1083 1067 1096 C5' G A 36 OK OK 1095 1115 1116 1097 1130 C5' C A 37 OK OK 1129 1146 1147 1131 1161 C5' A A 38 OK OK 1160 1179 1180 1162 1194 C5' A A 39 OK OK 1193 1212 1213 1195 1227 C5' A A 40 OK OK 1226 1245 1246 1228 1260 C5' A A 41 OK OK 1259 1278 1279 1261 1293 C5' A A 42 OK OK 1292 1311 1312 1294 1326 C5' U A 43 OK OK 1325 1342 1343 1327 1356 C5' C A 44 OK OK 1355 1372 1373 1357 1387 C5' A A 45 OK OK 1386 1405 1406 1388 1420 C5' U A 46 OK OK 1419 1436 1437 1421 1450 C5' U A 47 OK OK 1449 1466 1467 1451 1480 C5' A A 48 OK OK 1479 1498 1499 1481 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P U A 4 distorted distorted 75 98 99 100 127 P U A 5 distorted distorted 105 128 129 130 157 P C A 6 distorted distorted 135 158 159 160 189 P U A 7 distorted distorted 165 190 191 192 219 P U A 8 distorted distorted 197 220 221 222 249 P U A 9 distorted distorted 227 250 251 252 279 P U A 10 distorted distorted 257 280 281 282 309 P U A 11 distorted distorted 287 310 311 312 339 P A A 12 distorted distorted 317 340 341 342 372 P G A 13 distorted distorted 347 373 374 375 406 P U A 14 distorted distorted 380 407 408 409 436 P G A 15 distorted distorted 414 437 438 439 470 P A A 16 distorted distorted 444 471 472 473 503 P U A 17 distorted distorted 478 504 505 506 533 P U A 18 distorted distorted 511 534 535 536 563 P U A 19 distorted distorted 541 564 565 566 593 P U A 20 distorted distorted 571 594 595 596 623 P U A 21 distorted distorted 601 624 625 626 653 P C A 22 distorted distorted 631 654 655 656 684 P C A 23 distorted distorted 661 685 686 687 715 P A A 24 distorted distorted 692 716 717 718 748 P A A 25 distorted distorted 723 749 750 751 781 P A A 26 distorted distorted 756 782 783 784 814 P C A 27 distorted distorted 789 815 816 817 845 P C A 28 distorted distorted 822 846 847 848 876 P C A 29 distorted distorted 853 877 878 879 907 P C A 30 distorted distorted 884 908 909 910 938 P U A 31 distorted distorted 915 939 940 941 968 P U A 32 distorted distorted 946 969 970 971 998 P U A 33 distorted distorted 976 999 1000 1001 1028 P G A 34 distorted distorted 1006 1029 1030 1031 1062 P U A 35 distorted distorted 1036 1063 1064 1065 1092 P G A 36 distorted distorted 1070 1093 1094 1095 1126 P C A 37 distorted distorted 1100 1127 1128 1129 1157 P A A 38 distorted distorted 1134 1158 1159 1160 1190 P A A 39 distorted distorted 1165 1191 1192 1193 1223 P A A 40 distorted distorted 1198 1224 1225 1226 1256 P A A 41 distorted distorted 1231 1257 1258 1259 1289 P A A 42 distorted distorted 1264 1290 1291 1292 1322 P U A 43 distorted distorted 1297 1323 1324 1325 1352 P C A 44 distorted distorted 1330 1353 1354 1355 1383 P A A 45 distorted distorted 1360 1384 1385 1386 1416 P U A 46 distorted distorted 1391 1417 1418 1419 1446 P U A 47 distorted distorted 1424 1447 1448 1449 1476 P A A 48 distorted distorted 1454 1477 1478 1479 ---------------------------------------------------------------------------------